GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Halomonas xinjiangensis TRM 0175

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= reanno::psRCH2:GFF857
         (371 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  311 bits (797), Expect = 2e-89
 Identities = 174/359 (48%), Positives = 223/359 (62%), Gaps = 20/359 (5%)

Query: 1   MASVTLRDICKSYDGT-PITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGD 59
           MAS+ L  + K+Y G     + IDL+I DGEFVV VGPSGCGKSTLLR++AGLE IT G 
Sbjct: 1   MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60

Query: 60  LLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAE 119
           L ID++ VNDL P +R + MVFQ+YALYPHMTV  N+A+GLK   V + EI+RRV   A 
Sbjct: 61  LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120

Query: 120 ILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARL 179
           +L+++  LERKP+ LSGGQRQRVA+GR +VREP  FLFDEPLSNLDA LRVQMR+EI +L
Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180

Query: 180 HQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQM 239
            +R+++T +YVTHDQ+EA+TL D++VVLN G I QVG P+ +Y  P + FVA F+GSP M
Sbjct: 181 QRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAM 240

Query: 240 NFVEVRAISASPETVTIELPSGYPLTLPVDGSAVS-PGDPLTLGIRPE--HFVMPDEADF 296
           N                 LP  Y      +G       D   +GIRP+      PDE   
Sbjct: 241 NM----------------LPVAYLRERGANGLLDHLAADTDVIGIRPDDLRIEAPDEDHL 284

Query: 297 TFHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRE 355
              G + + E  G  + LY++LE       +       V EGET    +     H F +
Sbjct: 285 VVTGTVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPFNQ 343


Lambda     K      H
   0.322    0.139    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 369
Number of extensions: 16
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 371
Length of database: 354
Length adjustment: 29
Effective length of query: 342
Effective length of database: 325
Effective search space:   111150
Effective search space used:   111150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory